Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016143.1 Corchorus olitorius cultivar O-4 contig16176, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 7473
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:6009 original size:20 final size:21

Alignment explanation


    Indices: 5943--6012  Score: 70
    Period size: 22  Copynumber: 3.1  Consensus size: 21

       5933 AAAAATAAAG

                *           *     
       5943 AAAATATTTTTTCTTTTTCGCA
          1 AAAACATTTTTT-TTTATCGCA

                                     
       5965 AAAACAAATTTTTTTTTATGACGCA
          1 AAAAC--ATTTTTTTTTAT--CGCA

                                 
       5990 AAAAC-TTTTTTTTTATCGCA
          1 AAAACATTTTTTTTTATCGCA

               
       6010 AAA
          1 AAA

       6013 CCGAAATCTT


Statistics
Matches: 42,  Mismatches: 2, Indels: 10
        0.78            0.04        0.19

Matches are distributed among these distances:
  20    7  0.17
  22   15  0.36
  23    4  0.10
  24    7  0.17
  25    9  0.21

ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46


Consensus pattern (21 bp):   
AAAACATTTTTTTTTATCGCA

Found at i:6159 original size:31 final size:31

Alignment explanation


    Indices: 6097--6160  Score: 83
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       6087 AAACGCAGGA

                 *     *         *         
       6097 AAAAAGCAGGAGAAAGTTTTCCTTCCCCGGC
          1 AAAAACCAGGAAAAAGTTTTCATTCCCCGGC

                                *     *    
       6128 AAAAACCAGGAAAAAGTTTTTATTCCTCGGC
          1 AAAAACCAGGAAAAAGTTTTCATTCCCCGGC

              
       6159 AA
          1 AA

       6161 CGGCGCCAAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22


Consensus pattern (31 bp):   
AAAAACCAGGAAAAAGTTTTCATTCCCCGGC

Found at i:6354 original size:15 final size:15

Alignment explanation


    Indices: 6334--6364  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6324 GCAGAGGTTG

                           
       6334 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

                   *       
       6349 AAAGAAAGCAATTAA
          1 AAAGAAAACAATTAA

             
       6364 A
          1 A

       6365 CTAGAAACAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13


Consensus pattern (15 bp):   
AAAGAAAACAATTAA

Found at i:7250 original size:15 final size:15

Alignment explanation


    Indices: 7230--7260  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       7220 GCAGAGGTTG

                           
       7230 AAAGAAAACAATTAA
          1 AAAGAAAACAATTAA

                   *       
       7245 AAAGAAAGCAATTAA
          1 AAAGAAAACAATTAA

             
       7260 A
          1 A

       7261 CTAGAAACAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13


Consensus pattern (15 bp):   
AAAGAAAACAATTAA
Done.